v0.35.2

Turing v0.35.2

Diff since v0.35.1

Merged pull requests:

• Various CI improvements (#2375) (@penelopeysm)
• Fix the global Random.seed in runtests.jl (#2381) (@mhauru)
• Remove outdated version conditions (#2382) (@mhauru)
• Move ADTypeCheckContext tests to a separate module (#2383) (@mhauru)
• Bump Bijectors to 0.14.0 (#2384) (@penelopeysm)
• Don't get stuck in an infinite loop if HMC can't find an initial point (#2392) (@penelopeysm)

Closed issues:

• update() method for updating a fitted model with new data (#2308)
• Drop support for Tracker (#2356)
• Upgrade julia-actions/cache to v2 (#2370)
• AdvancedMH external-sampler tests fail intermittently with 2 threads (#2371)
• Use version = "min" in CI (#2373)
• Data transformation code slows down sampling? (#2380)
• New predict() behaviour and syntax? (#2388)
• Sampling with HMC can hang if AD is bugged (#2389)

v0.35.1

Turing v0.35.1

Diff since v0.35.0

• Bump Optimization compat to v4
• Bump DynamicPPL compat to v0.30.2

Merged pull requests:

• Bump Optimization to v4, and related packages accordingly (#2354) (@penelopeysm)
• Run JuliaFormatter on more files, remove trailing whitespace (#2374) (@mhauru)
• Bump DynamicPPL compat to 0.30 (#2376) (@penelopeysm)

v0.35.0

Turing v0.35.0

Diff since v0.34.1

• Drop support for Julia 1.9 and earlier. Minimum Julia version is now 1.10.
• Drop support for Tracker as an AD backend.
• Replace Tapir.jl with its reincarnated form, Mooncake.jl.

Merged pull requests:

• Widen Optimization compat to v4, and related packages accordingly (#2327) (@mhauru)
• CompatHelper: bump compat for DynamicPPL to 0.29, (keep existing compat) (#2339) (@github-actions[bot])
• CompatHelper: bump compat for DynamicPPL to 0.29 for package test, (keep existing compat) (#2340) (@github-actions[bot])
• DynamicPPL -> 0.29; Julia -> 1.10; Tapir -> Mooncake (#2341) (@penelopeysm)
• Revert changing Optimization compat to v4 (#2343) (@penelopeysm)
• Generate API docs (#2347) (@penelopeysm)
• Add issue templates (#2355) (@penelopeysm)
• Remove redundant code in hmc.jl (#2357) (@sunxd3)
• More autoformatting (#2359) (@mhauru)
• Update to tilde overloads in mh.jl (#2360) (@torfjelde)

Closed issues:

• Safety for poisson random calls (#2301)
• MLE estimation fails with error (#2342)
• Regenerate API docs (#2344)

v0.34.1

Turing v0.34.1

Diff since v0.34.0

Merged pull requests:

• Test with Tapir (#2289) (@mhauru)
• Update ad_utils.jl (#2313) (@yebai)
• Bump patch (#2314) (@willtebbutt)

Closed issues:

• Can DifferentiationInterface be useful for Turing? (#2187)
• Add an option to the sample function to force using SimpleVarInfo. (#2213)
• Add Tapir to Turing's AD test suite (#2247)
• Ensure that strictly positive distribution parameter is > 0 after exp() transformation (#2310)

v0.34.0

Turing v0.34.0

Diff since v0.33.3

Merged pull requests:

• Check that the correct AD backend is being used (#2291) (@mhauru)
• Resolve ADTypeCheckContext method ambiguity (#2299) (@mhauru)
• Fix remaining method ambiguities (#2304) (@penelopeysm)
• Remove unused code (#2312) (@devmotion)

Closed issues:

• Tests to check that the correct AD method is actually used (#2235)
• Enable Aqua.test_ambiguities (#2261)
• Mode estimation's support of Pathfinder integration (#2268)
• Multithread tests fail on master (#2302)
• Julia 1.7 tests are failing (#2305)
• Support potential type argument in rand for eltype of Sampleable (#2306)
• Dead code in mcmc/hmc.jl? (#2311)

v0.33.3

Turing v0.33.3

Diff since v0.33.2

Merged pull requests:

• Remove getmodel and setmodel after transferred to DynamicPPL (#2292) (@sunxd3)
• Add GITHUB_TOKEN permissions for format job (#2294) (@penelopeysm)
• Fix deprecated syntax error (#2297) (@sunxd3)

Closed issues:

• Attempt fixing bnn tests in Ezyme PR (#2277)
• Allow for a named tuple for initial_params (#2286)
• JuliaFormatter GHA workflow fails on public forks due to insufficient permissions (#2293)
• Turing fails to precompile due to deprecated method dispatches with v1.10 (#2296)

v0.33.2

Turing v0.33.2

Diff since v0.33.1

The release brought bug fixes and improvement to the new Experimental.Gibbs (👏 for @torfjelde 's heroic efforts)

Merged pull requests:

• Fixes and improvements to experimental Gibbs (#2231) (@torfjelde)
• Re-enable coverage uploads (#2283) (@devmotion)

Closed issues:

• Simple user error makes code evaluate forever - Calling DynamicPPL.Model as a function. (#2182)
• Experimental Gibbs seems to have higher variance than "stable" Gibbs (maybe) (#2230)
• Undeterministic test failure (#2234)
• Make MLE and MAP more robust (#2279)
• Fix code test coverage (#2282)
• preallocating an array of random variables, getting varname As used multiple times in model (subsumes As[1]) (#2284)
• maximum_likelihood function not found in Turing.jl (#2285)

v0.33.1

Turing v0.33.1

Diff since v0.33.0

Merged pull requests:

• Check model by default (#2218) (@torfjelde)
• disable more sampling progress logging on CI (#2254) (@yebai)
• Code formatting: JuliaFormatter (#2255) (@mhauru)
• Add note about breaking v0.33.0 changes to HISTORY (#2256) (@mhauru)
• Add Aqua to tests (#2257) (@mhauru)
• Remove trailing whitespace (#2260) (@mhauru)
• Update .JuliaFormatter.toml (#2262) (@yebai)
• Formatting VI files (#2263) (@yebai)
• CompatHelper: bump compat for OptimizationBBO to 0.3 for package test, (keep existing compat) (#2266) (@github-actions[bot])
• Bump SciMLBase compat lower bound (#2267) (@mhauru)
• Add Base.get method for ModeResult (#2269) (@mhauru)
• Use new style kwarg constructor for AutoReverseDiff (#2273) (@mhauru)
• Bump DynamicPPL to v0.28 (#2276) (@mhauru)
• Version bump 0.33+ (#2278) (@mhauru)

Closed issues:

• Feature Request: Better Indexing for ModeResult object (#1417)
• transform! not differentiable (#1835)
• Print an informational message about using ReverseDiff when the model size is above a certain threshold. (#1852)
• covariance matrix cannot be estimated using Wishart with NUTS, HMC or HMCDA samplers (#1861)
• ADVI example fails with Zygote AD backend (#1988)
• stderror() on optimize() result fails (#2048)
• Adopt Changelog.jl for tracking release notes and change logs (#2129)
• Documentation for optimisation methods (MAP, MLE) (#2164)
• Style Guide and Style Checker (#2241)
• Implementing adtype for closely linked "external" samplers / adding metric warm-up (#2248)
• Failing in precompiling dependencies (#2271)
• AbstractMCMC docs page out of date (#2272)

v0.33.0

Turing v0.33.0

Diff since v0.32.3

Merged pull requests:

• Reenable PriorContext for Optimization (#2165) (@alyst)
• Optimization improvements (#2221) (@mhauru)
• Test restructuring (#2237) (@mhauru)
• Update Project.toml (#2244) (@yebai)
• CompatHelper: bump compat for OptimizationOptimJL to 0.3 for package test, (keep existing compat) (#2246) (@github-actions[bot])
• Restore compat with ADTypes v0.2. Make AutoTapir export conditional. (#2252) (@mhauru)
• ADTypes v0.2 compatibility for test restructuring (#2253) (@mhauru)

Closed issues:

• refactor tests into multiple Github CI steps (#2179)
• Dependent uniform variables not working correctly (#2245)
• Compat issue (#2251)

v0.32.3

Turing v0.32.3

Diff since v0.32.2

Merged pull requests:

• Drop support for ADTypes 0.2 (#2243) (@yebai)